Ribosomal RNA pervades both ribosomal subunits

  • 5S RNA is a 120 base RNA that is a component of the large subunit of the ribosome.
  • 5.8S RNA is an independent small RNA present on the large subunit of eukaryotic ribosomes. It is homologous to the 5 end of bacterial 23S rRNA.
  • Each rRNA has several distinct domains that fold independently.
  • Virtually all ribosomal proteins are in contact with rRNA.
  • Most of the contacts between ribosomal subunits are made between the 16S and 23S rRNAs. 

Two thirds of the mass of the bacterial ribosome is made up of rRNA. The most penetrating approach to analyzing secondary structure of large RNAs is to compare the sequences of corresponding rRNAs in related organisms. Those regions that are important in the secondary structure retain the ability to interact by base pairing. So if a base pair is required, it can form at the same relative position in each rRNA. This approach has enabled detailed models to be constructed for both 16S and 23S rRNA.
Each of the major rRNAs can be drawn in a secondary structure with several discrete domains. 16S rRNA forms four general domains, in which just under half of the sequence is base paired (see Figure 6.45). 23S rRNA forms six general domains. The individual double-helical regions tend to be short (<8 bp). Often the duplex regions are not perfect, but contain bulges of unpaired bases. Comparable models have been drawn for mitochondrial rRNAs (which are shorter and have fewer domains) and for eukaryotic cytosolic rRNAs (which are longer and have more domains). The increase in length in eukaryotic rRNAs is due largely to the acquisition of sequences representing additional domains (for review see Noller, 1984). The crystal structure of the ribosome shows that in each subunit the domains of the major rRNA fold independently and have a discrete location in the subunit (Yusupov et al., 2001).
Differences in the ability of 16S rRNA to react with chemical agents are found when 30S subunits are compared with 70S ribosomes; also there are differences between free ribosomes and those engaged in protein synthesis. Changes in the reactivity of the rRNA occur when mRNA is bound, when the subunits associate, or when tRNA is bound. Some changes reflect a direct interaction of the rRNA with mRNA or tRNA, while others are caused indirectly by other changes in ribosome structure. The main point is that ribosome conformation is flexible during protein synthesis.
A feature of the primary structure of rRNA is the presence of methylated residues. There are ~10 methyl groups in 16S rRNA (located mostly toward the 3 end of the molecule) and ~20 in 23S rRNA. In mammalian cells, the 18S and 28S rRNAs carry 43 and 74 methyl groups, respectively, so ~2% of the nucleotides are methylated (about three times the proportion methylated in bacteria).
The large ribosomal subunit also contains a molecule of a 120 base 5S RNA (in all ribosomes except those of mitochondria). The sequence of 5S RNA is less well conserved than those of the major rRNAs. All 5S RNA molecules display a highly base-paired structure.
In eukaryotic cytosolic ribosomes, another small RNA is present in the large subunit. This is the 5.8S RNA. Its sequence corresponds to the 5 end of the prokaryotic 23S rRNA.
Some ribosomal proteins bind strongly to isolated rRNA. Some do not bind to free rRNA, but can bind after other proteins have bound. This suggests that the conformation of the rRNA is important in determining whether binding sites exist for some proteins. As each protein binds, it induces conformational changes in the rRNA that make it possible for other proteins to bind. In E. coli, virtually all the 30S ribosomal proteins interact (albeit to varying degrees) with 16S rRNA. The binding sites on the proteins show a wide variety of structural features, suggesting that protein-RNA recognition mechanisms may be diverse. 

The 70S ribosome has an asymmetric construction. Figure 6.36 shows a schematic of the structure of the 30S subunit, which is divided into four regions: the head, neck, body, and platform. Figure 6.37 shows a similar representation of the 50S subunit, where two prominent features are the central protuberance (where 5S rRNA is located) and the stalk (made of multiple copies of protein L7). Figure 6.38 shows that the platform of the small subunit fits into the notch of the large subunit. There is a cavity between the subunits which contains some of the important sites (for review see Wittman, 1983; Noller and Nomura, 1987; Hill et al., 1990).

The structure of the 30S subunit follows the organization of 16S rRNA, with each structural feature corresponding to a domain of the rRNA. The body is based on the 5 domain, the platform on the central domain, and the head on the 3 region. Figure 6.39 shows that the 30S subunit has an asymmetrical distribution of RNA and protein (Clemons et al., 1999; Wimberly et al., 2000). One important feature is that the platform of the 30S subunit that provides the interface with the 50S subunit is composed almost entirely of RNA. Only two proteins (a small part of S7 and possibly part of S12) lie near the interface. This means that the association and dissociation of ribosomal subunits must depend on interactions with the 16S rRNA. Subunit association is affected by a mutation in a loop of 16S rRNA (at position 791) that is located at the subunit interface, and other nucleotides in 16S rRNA have been shown to be involved by modification/interference experiments. This behavior supports the idea that the evolutionary origin of the ribosome may have been as a particle consisting of RNA rather than protein.
The 50S subunit has a more even distribution of components than the 30S, with long rods of double-stranded RNA crisscrossing the structure (Ban et al., 1999; Ban et al., 2000). The RNA forms a mass of tightly packed helices. The exterior surface largely consists of protein, except for the peptidyl transferase center (see 6.19 23S rRNA has peptidyl transferase activity). Almost all segments of the 23S rRNA interact with protein, but many of the proteins are relatively unstructured. 

The junction of subunits in the 70S ribosome involves contacts between 16S rRNA (many in the platform region) with 23S rRNA. There are also some interactions between rRNA of each subunit with proteins in the other, and a few protein-protein contacts. Figure 6.40 identifies the contact points on the rRNA structures. Figure 6.41 opens out the structure (imagine the 50S subunit rotated counterclockwise and the 30S subunit rotated clockwise around the axis shown in the figure) to show the locations of the contact points on the face of each subunit.